R/upSignalGraph.R

In saezlab/CNORfeeder: Integration of CellNOptR to add missing links

#
#  This file is part of the CNO software
#
#  Copyright (c) 2011-2012 - EBI
#
#  File author(s): CNO developers (cno-dev@ebi.ac.uk)
#
#  Distributed under the GPLv3 License.
#  See accompanying file LICENSE.txt or copy at
#      http://www.gnu.org/licenses/gpl-3.0.html
#
#  CNO website: http://www.cellnopt.org
#
##############################################################################
# $Id$
upSignalGraph <-
function(signal,graph,stopNodes){
  
  gg<-graph
  
  nod<-graph::nodes(gg)
  edg<-graph::edges(gg)
  
  SigUp<-signal
  
  findUp<-function(x){
    tmp<-vector()
    for (i in 1:length(nod)){
      if (any(edg[[i]]==x)){
         tmp<-c(tmp,nod[i])
      }
    }
    return(tmp)
  }
  
  tmp<-findUp(signal)
  tmp<-setdiff(tmp,stopNodes)
  queue<-tmp
  
  while (length(queue)>0){
    tmp<-findUp(queue[1])
    tmp<-setdiff(tmp,stopNodes)
    queue<-c(queue, tmp)
    SigUp<-c(SigUp,queue[1])
    queue<-setdiff(queue,SigUp)
    #queue<-queue[-1]
  }

  if (length(grep("and",SigUp))>0){
    SigUp<-SigUp[-grep("and",SigUp)]
  }
  return(SigUp)
}